Maloney was the first mate on a freighter haul on the Stellari captained by his old friend, Mari Tann. During the flight the ship somehow became overrun with Gatherers (which either killed the crew or converted them into more Gatherers). Tann and Maloney hid in a storeroom and tried to sneak past them, through the ship to the Bridge. They failed at avoiding the creatures and ended up being chased around the ship, getting mauled several times, and repeatedly running into two in the corridors they called "Jeffrey" and "Bob". As it happened, the freighter cargo included an Alfa Romeo, an ATV, and an army of police officers and clones of Finn the Human. Using these, the ship's supply of weapons, and a makeshift "Deathcoaster" comprised of the ATV and thrusters, they successfully retook the ship, though all of the Finns and some of the police officers were killed. The survivors were later picked up by space trucker John Canyon.

Following the destruction of the USS Voyager during the Romulan gambit to take the Derpian system, Maloney was drafted by Admiral Kickyourbottom to search for the Voyager. Knowing that his old friend Captain Tann was among those missing, Maloney volunteered immediately and was assigned to the USS Mirage, an experimental new ship designed for stealth missions.

At some point Maloney gained control of the USS Who's Your Mama 2. Admiral Jean-Luc Picard joined his crew, working as his mentor in some ways. Mari Tann also met Maloney again after escaping Romulan captivity. Other crewmembers, such as Sam Beltris, Adam Bridger, Rimmer, and Casey, joined Maloney's team and helped him on various missions. Maloney eventually promoted both Tann and Beltris to the ranks of commander, and appointed Beltris his own strike force.

Maloney is voiced by Nick "theglem4" Jacques. The character's first appearance was in the VenturianTale "Gmod STAR TREK Phaser Mod (Garry's Mod)" video, in which he was portrayed by Jordan "Venturian" Frye.